No they had to prove the players they were retaining were under the cap. There was no excess payments.
But there were excess payments. Because the payments paid to Cameron Smith in the first place were excess, because when Melbourne re-signed him, they were already over the salary cap at that particular point in time.
The fact that AFTER the fact they got themselves under the cap doesn't change the fact that they had Smith (and others) under false pretenses. Every single cent they paid these players were excess payments. Payments that the other 15 clubs in the league were not paying.
3 years ago, the NRL would not ratify a contract for Brett Stewart until Manly got themselves under the salary cap for the following season. They weren't allowed to sign him and then fix it up later. No, they needed to be in a cap compliant place before the signing was ratified. This never happened with Smith. Melbourne was then allowed to pick and choose who they kept and who they lost, and I'll say it again, despite having no standing under which to even offer these players contracts.
I read a story today about how Slater wanted to be a Cowboy. Who knows, if Melbourne had actually played by the rules, whether he may have left. Nobody can answer these questions, because they didn't play by the rules. The game was not fair, as 15 teams were playing under 1 set of rules, and 1 team was playing by their own. And they continue to prosper from that unfair game today.